Cell-signaling assays

ABSTRACT

Assays for detecting the presence and activity of cell-signaling components. These assays include luminescence polarization assays for detecting cell-signaling nucleotides and modulators of receptors and enzymes related to the generation and activity of such nucleotides.

CROSS-REFERENCES TO PRIORITY APPLICATIONS

This application is a continuation of U.S. patent application Ser. No.10/968,869, filed Oct. 18, 2004, which, in turn, is a continuation ofU.S. patent application Ser. No. 09/768,661, filed Jan. 23, 2001, nowU.S. Pat. No. 6,806,053, which, in turn, is a continuation of PCT PatentApplication Ser. No. PCT/US00/16012, filed Jun. 9, 2000, which, in turn,is based upon and claims priority under 35 U.S.C. §119 from thefollowing U.S. Provisional Patent Applications Ser. No. 60/200,594,filed Apr. 28, 2000; Ser. No. 60/182,036, filed Feb. 11, 2000; and Ser.No. 60/138,311, filed Jun. 9, 1999. These U.S., PCT, and provisionalpriority applications are incorporated herein by reference in theirentirety for all purposes.

CROSS-REFERENCES TO ADDITIONAL MATERIALS

This application incorporates by reference the following U.S. patentapplication Ser. Nos. 08/840,553, filed Apr. 14, 1997; Ser. No.08/929,095, filed Sep. 15, 1997; Ser. No. 09/118,141, filed Jul. 16,1998; Ser. No. 09/144,575, filed Aug. 31, 1998; Ser. No. 09/144,578,filed Aug. 31, 1998; Ser. No. 09/146,081, filed Sep. 2, 1998; Ser. No.09/156,318, filed Sep. 18, 1998; Ser. No. 09/160,533, filed Sep. 24,1998; Ser. No. 09/302,158, filed Apr. 29, 1999; Ser. No. 09/349,733,filed Jul. 8, 1999; Ser. No. 09/468,440, filed Dec. 21, 1999; Ser. No.09/478,819, filed Jan. 5, 2000; Ser. No. 09/494,407, filed Jan. 28,2000; and Ser. No. 09/556,030, filed Apr. 20, 2000.

This application also incorporates by reference the following PCT patentapplications Ser. No. PCT/US99/01656, filed Jan. 25, 1999; Ser. No.PCT/US99/03678, filed Feb. 19, 1999; Ser. No. PCT/US99/08410, filed Apr.16, 1999; Ser. No. PCT/US99/16057, filed Jul. 15, 1999; Ser. No.PCT/US99/16453, filed Jul. 21, 1999; Ser. No. PCT/US99/16621, filed Jul.23, 1999; Ser. No. PCT/US99/16286, filed Jul. 26, 1999; Ser. No.PCT/US99/16287, filed Jul. 26, 1999; Ser. No. PCT/US99/24707, filed Oct.19, 1999; Ser. No. PCT/US00/00895, filed Jan. 14, 2000; Ser. No.PCT/US00/03589, filed Feb. 11, 2000; Ser. No. PCT/US00/04543, filed Feb.22, 2000; Ser. No. PCT/US00/06841, filed Mar. 15, 2000; Ser. No.PCT/US00/12277, filed May 3, 2000; Ser. No. PCT/US00/16025, filed Jun.9, 2000; and Ser. No. PCT/US00/15774, filed Jun. 9, 2000.

This application also incorporates by reference the following U.S.provisional patent applications Ser. No. 60/138,438, filed Jun. 10,1999; Ser. No. 60/138,737, filed Jun. 11, 1999; Ser. No. 60/138,893,filed Jun. 11, 1999; Ser. No. 60/142,721, filed Jul. 7, 1999; Ser. No.60/143,185, filed Jul. 9, 1999; Ser. No. 60/153,251, filed Sep. 10,1999; Ser. No. 60/164,633, filed Nov. 10, 1999; 60/165,813, filed Nov.16, 1999; Ser. No. 60/167,301, filed Nov. 24, 1999; Ser. No. 60/167,463,filed Nov. 24, 1999; Ser. No. 60/178,026, filed Jan. 26, 2000; Ser. No.60/182,419, filed Feb. 14, 2000; Ser. No. 60/184,719, filed Feb. 24,2000; Ser. No. 60/184,924, filed Feb. 25, 2000; Ser. No. 60/190,265,filed Mar. 17, 2000; Ser. No. 60/191,890, filed Mar. 23, 2000; Ser. No.60/193,586, filed Mar. 30, 2000; Ser. No. 60/197,324, filed Apr. 14,2000; Ser. No. 60/200,530, filed Apr. 27, 2000; and Ser. No. 60/202,087,filed May 4, 2000.

This application also incorporates by reference the followingpublications: K. E. van Holde, Physical Biochemistry (2^(nd) ed. 1985);William Bains, Biotechnology from A to Z (1993); Richard P. Haugland,Handbook of Fluorescent Probes and Research Chemicals (6^(th) ed. 1996);Joseph R. Lakowicz, Principles of Fluorescence Spectroscopy (2^(nd) ed.1999); Bob Sinclair, Everything's Great When It Sits on a Chip: A BrightFuture for DNA Arrays 13 THE SCIENTIST, May 24, 1999, at 18; and CharlesR. Cantor and Paul R. Schimmel, Biophysical Chemistry (1980).

FIELD OF THE INVENTION

The invention relates to cell signaling. More particularly, theinvention relates to assays for detecting the presence and activity ofcell-signaling components, including cell-signaling nucleotides.

BACKGROUND OF THE INVENTION

Cellular physiology may be regulated by a variety of mechanisms,originating both inside and outside the cell. In multicellularorganisms, these mechanisms may involve cell-signaling pathways in whichsignal substances are released by one cell to influence the position,nature, and activity of other cells.

FIG. 1 is a schematic view of a representative cell-signaling pathway100. Here, signaling cells 102 produce signal substances 104 a,b thatinteract with target cells 106 to effect a response in the target cells.These responses may be short term, such as glycogen breakdown or musclecontraction, among others. These responses also may be long term, suchas growth, differentiation, reproduction, and/or apoptosis, amongothers. Generally, these responses are brought about by increasing,decreasing, or maintaining enzyme activity in the target cells.

Signaling cells 102 are cells capable of producing a signal (substance)that can effect a specific response in another (target) cell. Thesignaling cells may be components of an endocrine, paracrine, or nervoussystem. The endocrine system is an organism-wide control system thatregulates body function using hormones released by endocrine organs intothe bloodstream. The endocrine organs include the pituitary gland,thyroid gland, parathyroid glands, adrenal glands, thymus gland, pinealbody, pancreas, ovaries, testes, and kidneys. The paracrine system is alocal control system that regulates nearby cells using local mediatorsreleased into the extracellular medium. The nervous system is aspecialized control system that regulates specific cells usingelectrical impulses and neurotransmitters.

Signal substances 104 a,b are substances through which a signaling cellmay communicate with target cells, evoking a specific response. Signalsubstances may act as hormones, local mediators, and/orneurotransmitters, among others. Signal substances may take the form ofproteins, small peptides, amino acids, nucleotides, steroids (e.g.,cortisol, steroid sex hormones, vitamin D), retinoids, fatty acidderivatives, and dissolved gases (e.g., nitric oxide (NO) and carbonmonoxide (CO)), among others.

Target cells 106 are cells capable of responding to a specific signalsubstance produced by a signaling cell. The ability to respond maydepend on the cell and on the signal substance. For example, the signalsubstance thyroxine from the thyroid gland may evoke a response innearly all cells, whereas the signal substance progesterone from theovary may evoke a response only in specific cells in the lining of theuterus. The target response may include kinase activity, GTP binding,and/or cyclic nucleotide production.

The ability of a cell to respond to a given signal substance generallyis determined by whether the cell includes a receptor for the signalsubstance. Here, a receptor is any molecule or supramolecular assemblycapable of specifically binding a signal substance and initiating aresponse in a target cell. Representative receptors include cell-surfacereceptors 110 located on the surface of the target cell andintracellular receptors 112 located within the cytosol 114 or nucleus116 of the target cell.

The nature of the response initiated by binding of a signal substance isdetermined by the intracellular machinery to which the receptor isoperatively coupled. For example, binding of the neurotransmitteracetylcholine to identical receptors in heart muscle cells and secretorycells causes muscle relaxation in the heart muscle cells and secretionin the secretory cells, due to differences in the associatedintracellular machinery.

The remainder of this section examines (1) the receptor mechanisms thatcells use to bind signal substances and to communicate this binding tothe cell interior, (2) the intracellular pathways that cells use forregulation, and (3) the effects of errors in cell-signaling pathways.

1. Receptor Mechanisms

Target cells generally have receptors capable of specifically bindingspecific signal substances, including cell-surface receptors and/orintracellular receptors, as described above. Cell-surface receptors aremore common and include (A) G-protein-linked receptors, (B)enzyme-linked receptors, and (C) ion-channel-linked receptors. Thesereceptors typically bind large and/or water-soluble signal substances,such as many peptide hormones. Intracellular receptors are less commonand include (A) guanylyl cyclase and (B) ligand-activated generegulatory proteins. These receptors typically bind small and/orwater-insoluble signal substances, such as steroid hormones, thyroidhormones, retinoids, vitamin D, and NO.

FIG. 2 is a schematic view of a representative G-protein-linkedcell-surface receptor mechanism 130 that includes a receptor protein132, a G-protein 134, and a target protein 136. These proteins may bepositioned on or within the plasma membrane 138 of a target cell. Inuse, a specific signal substance 140 binds to a signal-substance bindingsite 142 on the extracellular side 144 of the receptor protein andthereby creates, exposes, or otherwise activates (*) a G-protein bindingsite 146 on the intracellular side 148 of the receptor protein. TheG-protein then binds to the G-protein binding site on the receptorprotein and thereby creates, exposes, or otherwise activates (*) atarget-protein binding site 150 on the G-protein. The G-protein thendissociates from the receptor protein, binds (via the target-proteinbinding site) to the target protein, and activates (*) the targetprotein. Activation and deactivation of the G-protein may involvebinding of a guanosine triphosphate (GTP) molecule and dephosphorylationof the GTP molecule, respectively. The receptor protein may belong to alarge superfamily of homologous, seven-pass transmembrane proteins.These seven-pass proteins consist of a single polypeptide chain thatcrosses the membrane seven times, with an extracellular signal-substancebinding portion and an intracellular catalytic portion. The G-proteinmay be trimeric, consisting of three polypeptide chains α, β, and γ—thatassociate and dissociate during signaling. The target protein mayconsist of an enzyme or ion channel, among others. In particular, thetarget protein may be an enzyme that modulates the presence or activityof second messengers within the cell. These second messengers (alsoknown as intracellular messengers or intracellular mediators) may bindallosterically to specific cellular proteins to alter their conformationand hence their activity. These second messengers include adenosine3′,5′-cyclic monophosphate (cAMP) and calcium (Ca²⁺).

In the cAMP pathway, the target protein may be adenylyl cyclase (alsoknown as adenylate cyclase), and the G-protein may be a stimulatoryG-protein (G_(s)) that activates the adenylyl cyclase to make cAMP, oran inhibitory G protein (G) that inhibits the adenylyl cyclase toprevent it from making cAMP. The cAMP produced by the adenylyl cyclaseactivates cAMP-dependent protein kinase (A-kinase), which is aserine/threonine kinase that in turn activates or inhibits other enzymesto effect a physiological response. For example, in connection withglycogen metabolism, A-kinase may inhibit glycogen synthase to shut downglycogen synthesis, and simultaneously activate phosphorylase kinasethat in turn activates glycogen phosphorylase to break down glycogen. Avariety of signal substances use cAMP as a second messenger, includingcalcitonin, chorionic gonadotropin, corticotropin, epinephrine,follicle-stimulating hormone, glucagon, luteinizing hormone, lipotropin,melanocyte-stimulating hormone, norepinephrine, parathyroid hormone(PTH), thyroid-stimulating hormone, and vasopressin. The level of cAMPis reduced by phosphodiesterases, and the activity of kinases isreversed by phosphatases, as described below.

In the Ca²⁺ pathway, the target protein may be a phospholipase withspecificity for a phosphoinositide (i.e., inositol phospholipid), andthe G-protein may be G_(q), which activates the phospholipase to cleavethe phosphoinositide to produce an intermediate that releases Ca²⁺ fromthe endoplasmic reticulum. For example, the phospholipasephosphoinositide-specific phospholipase C (phospholipase C-3) cleavesthe phosphoinositide phosphatidylinositol 4,5-bisphosphate (PIP₂) toproduce the second messengers inositol triphosphate (IP₃) anddiacylglycerol. The inositol triphosphate is water soluble and diffusesto the endoplasmic reticulum (ER), where it releases Ca²⁺ from the ER bybinding to IP₃-gated Ca²⁺-release channels in the ER membrane. Thediacylglycerol is membrane bound and may be cleaved to form the secondmessenger arachidonic acid or may activate the Ca²⁺-dependentserine/threonine kinase protein kinase C that in turn activates orinhibits other enzymes to effect a response. A variety of signalsubstances use Ca²⁺ as a second messenger, including acetylcholine,antigen, thrombin, and vasopressin.

FIG. 3 is a schematic view of a representative enzyme-linkedcell-surface receptor mechanism 170 that includes a receptor protein 172positioned across the plasma membrane 174 of a target cell. The receptorprotein includes a signal-substance binding site 176 on theextracellular side 178 of the membrane and a catalytic portion 180 onthe intracellular side 182 of the membrane. (In some cases, thecatalytic portion of the receptor may be replaced or augmented by aseparate enzyme directly associated with the receptor protein.) In use,a specific signal substance 184 binds to the signal-substance bindingsite, initiating a series of events (such as dimerization andconcomitant autophosphorylation of the receptor proteins) that activates(*) the catalytic portion of the receptor. The receptor protein maybelong to one of at least five classes of single-pass transmembraneproteins: (A) receptor guanylyl cyclases, which catalyze the productionof guanosine 3′,5′-cyclic monophosphate (cGMP) in the cytosol; (B)receptor tyrosine kinases, which phosphorylate specific tyrosineresidues on some intracellular proteins, (C) tyrosine-kinase-associatedreceptors, which associate with proteins that phosphorylate specifictyrosine residues on some intracellular proteins; (D) receptor tyrosinephosphatases, which dephosphorylate specific tyrosine residues on someintracellular proteins, and (E) receptor serine/threonine kinases, whichphosphorylate specific serine or threonine residues on someintracellular proteins. Some of these receptors are described below inmore detail.

The signal substance also may bind to intracellular receptors, such asguanylyl cyclase. This enzyme produces cGMP from GTP, which then acts asa second messenger much like cAMP. As described above, cGMP also may beproduced by enzyme-linked cell-surface receptors. cGMP is present inmost tissues at levels 1/10 to 1/100 those of cAMP. A variety ofcompounds increase cGMP levels in cells, including (1) the hormonesacetylcholine, insulin, and oxytocin, (2) the guanylate cyclasestimulators (and vasodilators) nitroprusside, nitroglycerin, sodiumnitrate, and nitric oxide, (3) chemicals such as serotonin andhistamine, and (4) peptides such as atrial natriuretic peptide (ANP)that relax smooth muscle.

2. Intracellular Signaling Pathways

Target cells may have intracellular signaling pathways capable ofspecifically binding signal substances, including cell-surface receptorsand intracellular receptors, as described above. These pathways mayinclude (1) a phosphorylation pathway involving ATP/ADP, and (2) aGTP-binding pathway involving GTP/GDP.

FIG. 4A is a schematic view of a representative phosphorylation pathway.Phosphorylation is the predominant mechanism used to regulate proteinactivity in eucaryotic cells. In phosphorylation, a phosphate group (P)is reversibly attached to the side chain of an amino acid in a protein.The attached phosphate group may cause structural changes in theprotein, for example, due to electrostatic interactions between thenegative charges on the phosphate group and positive charges on the sidechains of nearby amino acids. These structural changes may affect theactivity of the phosphorylated protein, enhancing or inhibiting itsfunction.

Specialized enzymes control phosphorylation in cells. In particular,protein kinase enzymes transfer phosphate groups to proteins, andprotein phosphatase enzymes remove phosphate groups from proteins.Protein kinases and protein phosphatases are found in great variety ineucaryotic cells: a single cell may contain more than 100 differentkinases, and one percent of genes may code for kinases.

There are two major categories of kinases: (1) serine/threonine (S/T)kinases, and (2) tyrosine kinases. The S/T kinases function byselectively phosphorylating serine and threonine side chains onsubstrate proteins or peptides. These kinases include cyclicAMP-dependent kinase (A-kinase), cyclic GMP-dependent kinase (G-kinase),protein kinase C(C-kinase), Ca²⁺-calmodulin-dependent kinase(CaM-kinase), phosphorylase kinase, MAP kinase, and TGF-β receptor,among others. The S/T kinases are predominantly cytosolic. The tyrosinekinases function by selectively phosphorylating tyrosine side chains onsubstrate proteins or peptides. These kinases include the receptorkinases for epidermal growth factor (EGF), platelet-derived growthfactor (PDGF), fibroblast growth factors (FGFs), hepatocyte growthfactor (HGF), insulin, insulinlike growth factor-1 (IGF-1), nerve growthfactor (NGF), vascular endothelial growth factor (VEGF), and macrophagecolony stimulating factor (M-CSF). These kinases also include thenonreceptor kinases associated with the tyrosine-kinase-associatedreceptors, such as the Src family (Src, Yes, Fgr, Fyn, Lck, Lyn, Hck,and Blk) and Janus family (JAK1, JAK2, and Tyk2) kinases. The tyrosinekinases are predominantly membrane bound. A few kinases function byselectively phosphorylating threonine and tyrosine side chains onsubstrate proteins or peptides. These kinases include themitogen-activated protein (MAP) kinase-kinase.

FIG. 4B is a schematic of a representative GTP-binding pathway. TheGTP-binding pathway generally resembles the phosphorylation pathway inthat each pathway involves transfer of a phosphate group to a protein.However, in the GTP-binding pathway, the protein gains a phosphate groupby exchanging a bound GDP for a bound GTP, whereas in thephosphorylation pathway, the protein gains a phosphate group by covalentaddition of the phosphate group to a serine, threonine, or tyrosine by akinase enzyme. The binding of a GTP to a GTP-binding protein may causestructural changes in the protein that in turn affect the activity ofthe protein. Examples of GTP-binding proteins include the trimericG-proteins described above and the Ras superfamily of monomeric GTPases.The Ras proteins are activated by release of bound GDP and binding ofGTP stimulated by guanine-nucleotide releasing proteins (GNRPs). The Rasproteins are inactivated by hydrolysis of the bound GTP byGTPase-activating proteins (GAPs).

A physiological response may require stimulation by only a single typeof signal substance, or may require stimulation by two or more types ofsignal substances. The latter mechanism permits finer tuning of thephysiological response through signal integration. For example, aprotein may be activated only by phosphorylation by two differentkinases, themselves activated by binding of two different signalsubstances to two different receptors. Alternatively, a protein may beactivated only by concurrent phosphorylation and GTP binding, or bybinding of two subunits whose binding is contingent on phosphorylationby separately activated kinases.

3. Effects of Errors

Errors in the signal transduction and regulation pathways describedabove can cause cancer and other diseases. Indeed, a primary cause ofcancer is a mutation that makes a stimulatory gene product hyperactive,converting a proto-oncogene into an oncogene. The primary classes ofknown proto-oncogenes include the following cell-signaling proteins: (1)growth-factor receptors acting via tyrosine kinases, (2) GTP bindingproteins, (3) membrane/cytoskeleton-associated tyrosine kinases, (4)cytoplasmic tyrosine kinases, (5) steroid-type growth-factor receptors,and (6) S/T kinases. Consequently, cell-signaling proteins have becomeimportant subjects of research and drug development.

Assays that determine the presence and activity of cell-signalingcomponents are important tools for high-throughput screeninglaboratories. Unfortunately, current assays have a number ofshortcomings. For example, the presence and activity of kinases can bedetermined using assays capable of detecting phosphorylated amino acids.In a standard kinase assay, radioactive ATP and an appropriate proteinsubstrate are added to a sample. If the sample includes kinases,radioactive phosphate groups will be transferred from the radioactiveATP to the protein substrate. The protein substrate and radioactive ATPcan be separated, and the presence and activity of kinases determined byassaying the amount of radioactive protein substrate. Unfortunately,this assay involves radioactivity, presenting a short-term safety hazardfor the assay operator and a long-term storage and disposal problem.Moreover, the assay is heterogeneous, requiring separation of componentsfor analysis. Significantly, assays for other cell-signaling componentsmay have similar shortcomings, as well as slow time courses and unstableendpoints that require precise timing of assay readouts. Thus, there isa need for improved assays for detecting the presence and activity ofcell-signaling components.

SUMMARY OF THE INVENTION

The invention provides improved assays for detecting the presence andactivity of cell-signaling components. These assays include luminescencepolarization assays for detecting cell-signaling nucleotides andmodulators of receptors and enzymes related to the production andactivity of such nucleotides.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a schematic view of a cell-signaling pathway.

FIG. 2 is a schematic view of a G-protein-linked cell-surface receptormechanism that includes a receptor protein, a G-protein, and a targetprotein, all associated with the plasma membrane of a target cell.

FIG. 3 is a schematic view of an enzyme-linked cell-surface receptormechanism that includes a receptor protein positioned across the plasmamembrane of a target cell.

FIG. 4 is a schematic view of two common intracellular signalingpathways: (A) a phosphorylation pathway involving ATP/ADP, and (B) aGTP-binding pathway involving GTP/GDP.

FIG. 5 is a schematic view of a cyclic nucleotide assay in accordancewith aspects of the invention.

FIG. 6 is a schematic view of a GTP-binding protein assay in accordancewith aspects of the invention.

FIG. 7 is a view of representative cAMP tracers constructed inaccordance with aspects of the invention: (A)fluorescein-ITC-1,4-DACHsuccinimidyl cAMP andfluorescein-ITC-1,2-DACHsuccinimidyl cAMP, and (B)carboxyfluorescein-ITC-1,4-DACHsuccinimidyl cAMP andcarboxyfluorescein-ITC-1,2-DACHsuccinimidyl cAMP.

FIG. 8 is a view of representative cGMP tracers constructed inaccordance with aspects of the invention: (A)fluorescein-ITC-1,4-DACHsuccinimidyl cGMP andfluorescein-ITC-1,2-DACHsuccinimidyl cGMP, and (B)carboxyfluorescein-ITC-1,4-DACHsuccinimidyl cGMP andcarboxyfluorescein-ITC-1,2-DACHsuccinimidyl cGMP.

FIG. 9 is a schematic view of a microplate showing a well layout for acAMP assay, including positions of samples, calibrators, and controls:(A) well layout page 1, and (B) well layout page 2.

FIG. 10 is a calibration curve for a cAMP assay.

FIG. 11 is a calibration curve for a cGMP assay.

FIG. 12 is a graph showing another application of a cAMP assay todetection of adenylyl cyclase activity in a membrane preparation.

FIG. 13 is a graph showing an application of the cAMP assay to theeffects of modulators in a whole cell preparation.

DETAILED DESCRIPTION

The invention provides improved assays for detecting the presence andactivity of cell-signaling components. These assays include among othersluminescence polarization assays for detecting cyclic nucleotides andmodulators of receptors and enzymes related to the generation andactivity of cyclic nucleotides, such as GTP-binding proteins.

FIG. 5 is a schematic view of a cyclic nucleotide assay provided by theinvention. Here, a sample containing a cyclic nucleotide (analyte) iscontacted with a luminescent tracer and a binding partner capable ofspecifically and competitively binding the cyclic nucleotide and theluminescent tracer. Suitable analytes, tracers, and binding partners aredescribed below; representative examples include cAMP and cGMP,luminescently labeled cAMP and cGMP, and anti-cAMP and anti-cGMPantibodies, respectively. The analyte will reduce the amount of tracerbound to the binding partner, because the analyte will compete with thetracer for the limited number of binding sites associated with thebinding partners. The change in free and bound tracer can be monitoredusing luminescence polarization. Free tracer is small and will tumble orreorient rapidly relative to the luminescence lifetime, so that it willemit relatively depolarized light in response to excitation withpolarized light. In contrast, bound tracer is large and will tumble orreorient more slowly relative to the luminescence lifetime, so that itwill emit relatively polarized light in response to excitation withpolarized light. Thus, the extent of polarization will be inverselycorrelated with the concentration of analyte, and the displacement ofthe tracer from the binding partner by the analyte will result in adecrease in polarization.

The invention provides luminescence-based methods for determining theconcentration of various cyclic nucleotides. Such methods may include(1) contacting a sample in which the concentration of a cyclicnucleotide is to be measured with a luminescent tracer and with aspecific binding partner capable of specifically and competitivelybinding the cyclic nucleotide and tracer, (2) illuminating the samplewith polarized light, where the light is capable of inducing emission ofpolarized light from the tracer, (3) measuring the extent ofpolarization of light emitted from the tracer, and (4) correlating theextent of polarization of the emitted light with the concentration ofthe cyclic nucleotide.

The invention also provides methods for identifying modulators ofreceptors and/or enzymes involved in the generation of cyclicnucleotides. Such methods may include looking for the effects of such amodulator by conducting a method for determining the concentration of acyclic nucleotide (such as that described above) in both the presenceand absence of the putative modulator. In this approach, an increase inthe measured extent of polarization of the emitted light in the presenceof the putative modulator identifies the putative modulator as aninhibitor of the receptor or enzyme, and a decrease in the measuredextent of polarization in the presence of the putative modulatoridentifies the putative modulator as an agonist of the receptor orenzyme.

Stated differently, the concentration of a signaling intermediate (e.g.,a cyclic nucleotide) may be used as an index to the activity of theenzyme(s) (directly or indirectly) catalyzing production of theintermediate, or as an index to an agonist with regard to that activityor an inhibitor with regard to that activity. If the enzyme isassociated with a receptor, the assay effectively measures the abilityof a candidate or test compound to act as an agonist or antagonist ofthe receptor, modulating activity of the receptor. Thus, the assays ofthe invention provide a broad spectrum of assessment to evaluatecell-signaling, metabolism, catalytic activities, and protein synthesis.

FIG. 6 is a schematic view of a GTP-binding protein assay provided bythe invention. Here, a sample containing a putative modulator of aGTP-binding protein is contacted with a GTP-binding protein, GDP, and aluminescent GTP tracer. If the modulator activates (*) the GTP-bindingprotein, the GDP will be released, and the GTP tracer will be bound. Ina polarization assay, the polarization of light emitted by the tracerwill increase upon such binding, because the rotational mobility of theGTP tracer will be reduced. This increase may be used to assay for theextent of binding and hence the activity or effectiveness of theputative modulator.

Samples and assay components such as tracers and binding partners may bebrought into contact using any method for effectuating such contact. Apreferred method is by mixing the materials in solution, although othermethods, such as attaching one or more components to a bead or surface,also may be used, as long as the components retain at least somespecificity and binding affinity following such attachment.

Samples may be supported for analysis by any substrate or materialcapable of providing such support. Depending on the embodiment, suitablesubstrates include microplates, PCR plates, biochips, and hybridizationchambers, among others, where features such as microplate wells andbiochip array sites may comprise assay sites. Preferred microplates aredescribed in the following U.S. patent applications, which areincorporated herein by reference: Ser. No. 08/840,553, Ser. No.09/156,318, and Ser. No. 09/478,819. These microplates may include 96,384, 1536, or other numbers of wells. These microplates also may includewells having elevated bottoms, small (≦50 μL) volumes, and/orfrusto-conical shapes capable of matching a sensed volume. Preferred PCRplates may include the same (or a similar) footprint, well spacing, andwell shape as the preferred microplates, while possessing stiffnessadequate for automated handling and thermal stability adequate for PCR.Preferred DNA arrays are described in Bob Sinclair, Everything's GreatWhen It Sits on a Chip: A Bright Future for DNA Arrays, 13 THESCIENTIST, May 24, 1999, at 18. Preferred hybridization chambers aredescribed in PCT Patent Application Ser. No. PCT/US99/03678, which isincorporated herein by reference.

Samples may be illuminated and light from samples may be detected usingany suitable light detection device, particularly one capable ofinducing and detecting polarized emission from the sample. Preferredlight detection devices include a high color temperature light sourceand are capable of illuminating and/or detecting light substantiallyexclusively from a sensed volume within the sample. Additional featuresof the preferred light detection devices, including apparatus anddetection methods, are described in the following U.S. patentapplications, which are incorporated herein by reference: Ser. No.09/160,533, and Ser. No. 09/349,733.

The extent of polarization of light emitted from the sample may becorrelated with the concentration of cyclic nucleotide and/or thepresence and/or identity of a modulator of a receptor or enzyme thatgenerates a cyclic nucleotide using various methods. A preferred methodis to compute a polarization or anisotropy function following acompetition assay, wherein the polarization and anisotropy of theemitted light are inversely correlated with the concentration of thecyclic nucleotide. Apparatus and methods for creating, detecting, and/orinterpreting results obtained using polarized light are described in theExamples that appear below and in the following patent applications,which are incorporated herein by reference: U.S. patent application Ser.No. 09/349,733, and U.S. Provisional Patent Application Ser. No.60/182,419.

The assays provided by the invention may have various advantages overprior assays for detecting cyclic nucleotides. First, they may be usedwithout radioactivity. Second, they may be homogenous, so that they donot require physical separation steps or wash steps. Third, they mayhave stable endpoints, so that results are relatively insensitive to thetiming of any measurement or detection steps. Fourth, they may besensitive, so that pmol amounts of cyclic nucleotides may be detected.Fifth, they may be used with solution and cell-based samples.

Further aspects of the invention are described without limitation in thepatent applications and other materials incorporated by reference underCross-References and in the following sections: (A) Assay Components,and (B) Examples.

A. Assay Components

The invention in its various aspects may include and/or involve amongothers one or more of the following: (1) analytes, (2) tracers, (3)specific binding partners, and (4) modulators. The format of the assaymay place constraints on the preferred relative concentrations ofanalyte, tracer, and specific binding partner and on the preferredlifetime of the luminophore associated with the tracer. For example, ina competition assay, the concentration of binding partner is preferablyat least about equal to the concentration of tracer (to permitstoichiometrically an appreciable fraction of the tracer to be bound),and the affinity of the binding partner for the tracer is preferablysuch that the dissociation coefficient K_(d) describing interactionbetween the binding partner and tracer is about equal to theconcentration of the free binding partner (so that the fraction of boundtracer is not too close either to 0 or 1, to maximize sensitivity).Moreover, the lifetime of the luminophore associated with the tracerpreferably is longer than the rotational correlation time of free tracerand shorter than the rotational correlation time of bound tracer, and,all else being equal, ideally equal to the geometric mean of the tworotational correlation times of free and bound tracer (to obtain thelargest polarization change upon binding).

1. Analytes

The analyte generally comprises any compound or other species whosepresence, concentration, and/or activity is to be assayed. For example,the analyte in a cyclic nucleotide assay is a cyclic nucleotide, such asthe following:

Abbreviation Definition cAMP Adenosine cyclic monophosphate cCMPCytidine cyclic monophosphate cGMP Guanosine cyclic monophosphate cTMPThymidine cyclic monophosphate cUMP Uridine cyclic monophosphatePreferred cyclic nucleotide analytes include cAMP and cGMP, which areused by cells as second messengers in various intracellular signalingpathways.

An analyte may be one of several components in a sample being analyzed.A sample generally comprises any composition in which the concentrationof analyte is to be measured, and/or in which the presence and/oridentity of a modulator of receptors or enzymes that generate theanalyte is to be measured. The sample may be natural, artificial, or acombination thereof, and may include compounds, compositions, mixtures,surfaces, solutions, emulsions, suspensions, cells, cell cultures,fermentation cultures, tissues, secretions, and/or derivatives and/orextracts thereof, among others. Assays of purified enzyme, cell lysates,and so on generally will require optimization and validation based uponthe requirements of the individual test systems.

2. Tracers

The tracer generally comprises any luminescent compound or other speciescapable of competing with the analyte for binding to a specific bindingpartner. A preferred tracer may be the analyte itself coupled to aluminophore. For example, in a cyclic nucleotide assay, a preferredtracer is a cyclic nucleotide coupled to a luminophore.

The luminophore may include any compound capable of emitting light inresponse to excitation with light, and more particularly of emittingpolarized light in response to excitation with polarized light. Suitableluminophores are described in Richard P. Haugland, Handbook ofFluorescent Probes and Research Chemicals (6^(th) ed. 1996), which isincorporated herein by reference. Preferred luminophores includexanthene dyes such as fluorescein and various rhodamines, BODIPY™ dyes,cyanine dyes such as CY-5™, and others, including luminophores describedin patent applications listed above under Cross-References, which areincorporated herein by reference.

The luminophore may be coupled to the analyte covalently ornoncovalently. Luminophores may be coupled covalently (for example, tothe 2′ hydroxyl) using various reactive groups, including amines,carboxylic acids, isothiocyanates, hydrazides, thiols, maleimides anddichlorotriazinyl derivatives. Luminophores may be coupled noncovalentlyusing various specific binding pairs, including avidin and biotin,protein A and immunoglobulins, and lectins and sugars (e.g.,concanavalin A and glucose). In preferred polarization tracers, theluminophore is coupled to the analyte by a rigid coupling group, such asa diaminocyclohexyl coupling group.

Preferred tracers will undergo a significant change in polarization uponbinding to a preferred binding partner, and will have high extinctioncoefficients, intrinsic polarizations, quantum yields, and/or Stokes'shifts.

3. Specific Binding Partners

The specific binding partner generally comprises any compound capable ofspecifically and competitively binding an analyte and an associatedtracer. Specific binding means binding to the specific binding partnerto the exclusion of binding to most other moieties. Specific binding canbe characterized by a binding coefficient. Generally, specific bindingcoefficients range from 10⁻⁴ M to 10⁻¹² M and lower, and preferredspecific binding coefficients range from 10⁻⁹ M to 10⁻¹² M and lower.

In some assays, fragments, derivatives, or analogs of a preferredspecific binding partner may be used, if such fragments, derivatives,and analogs retain their specificity and binding affinity for theirbinding partners. In other assays, such fragments, derivatives, andanalogs, or the specific binding partners themselves, may be coupled tosolid supports or other moieties, including beads and walls.

Preferred specific binding partners include immunological specificbinding partners, such as antibodies. Such preferred binding partnerswill bind to the cyclic nucleotide of interest, independent of whetherthe cyclic nucleotide is coupled to a luminophore. However, suchcoupling may affect the coefficient of such binding. Immunologicalbinding partners include polyclonal and monoclonal antibodies.Immunological binding partners also include chimeric, single chain, andhumanized antibodies, as well as Fab fragments and the products of Fabexpression libraries.

Immunological binding partners, including antibodies and fragments,analogs, and/or derivatives of such antibodies, can be prepared byvarious generally known procedures. For example, antibodies againstcyclic nucleotides can be obtained by injecting or otherwiseadministering a suitable immunogen into an animal. Suitable immunogensmay include the cyclic nucleotide itself, fragments, analogs, and/orderivatives thereof, or cells expressing such cyclic nucleotides,fragments, analogs, and/or derivatives. The antibody so obtained shouldspecifically bind to the cyclic nucleotide.

Monoclonal antibodies can be prepared by any technique that providesantibodies produced by continuous cell line cultures. Examples includethe hybridoma technique (Köhler and Milstein, Nature 256:495 (1975)),the trioma technique, the human B-cell hybridoma technique (Kozbor etal., Immunology Today 4:72 (1983)), and the EBV-hybridoma technique toproduce human monoclonal antibodies (Cole et al., in MonoclonalAntibodies and Cancer Therapy, Alan R. Liss, p. 77 (1985)).

Single-chain antibodies can be prepared using any technique forproducing single-chain antibodies. Examples include the method describedin U.S. Pat. No. 4,946,778.

4. Modulators

The modulator generally comprises any compound or other species capableof modulating the activity of receptors, enzymes, and/or other speciesinvolved in the generation of analyte. The modulator may be an agonistor an inhibitor of analyte production, meaning that it may promote orinhibit analyte production. For example, in a cyclic nucleotide assay,preferred agonists include forskolin and isoproterenol, and preferredinhibitors include propranolol.

B. EXAMPLES

The following examples are intended to illustrate without limitationvarious aspects of the invention.

Example 1

This example shows representative tracers for use in cyclic nucleotideassays, and particularly luminescence-polarization-based cyclicnucleotide assays. General structures for such tracers are shown belowfor (A) cAMP and (B) cGMP:

X can be any alkyl, allyl, or aryl linker with ester or ether bonds tothe cyclic nucleotide, including —OC(═O)—CH₂CH₂C(═O)—. R1 can be a rigidlinker that provides (two) reactive groups for coupling, one to thenucleotide and another to the group Fl. In particular, R1 can be adiamino-alkyl, -cycloalkyl, -aryl, or -allyl group, or a dihydroxygroup, that forms an amide or ester, respectively, with the groups X andFl. Fl can be any luminophore suitable for polarization, such asfluorescein or a rhodamine, that forms a thiourea, ester, or amide bondwith the group X. Preferred Structures Include 1,2 and1,4-diaminocyclohexyl-linked tracers, as shown in FIG. 7 for cAMP andFIG. 8 for cGMP.

Example 2

This example shows a mechanism for producing specific binding partners.Specifically, antisera to cAMP were produced by conjugating2′o-succinyl-cyclic 3′,5′ adenosine monophosphate to the carrier KLHusing standard methods, and using this conjugate as an immunogen.Preparation of antisera in rabbits was done according to an enhancedmethod of antibody production, using low (25 μg per injection) doses ofimmunogen to enhance the immune response. Antisera obtained using thisapproach were superior to commercial antisera.

Example 3

This example shows a method (and associated kit) for detecting cAMP andmodulators of receptors and enzymes that generate cAMP. Specifically,the assay is designed for use in applications where cAMP is generated orconsumed, such as adenylyl cyclase or phosphodiesterase assays. Theassay may be used to detect cAMP or the activity of adenylyl cyclase orphosphodiesterase, among others, through their effect on cAMPconcentration, via a competitive luminescence-polarization immunoassay.The assay is homogeneous, requiring no separation or wash steps, and canbe completed in two hours. The cAMP product of an adenylyl cyclasereaction (or substrate of a phosphodiesterase reaction, or calibrators,or controls) competes with a fluorescein-labeled cAMP tracer(fluorescein-5-ITC-DACHsuccinimidyl-cAMP) for binding sites on anti-cAMPantibodies. In the absence of cAMP, most of the tracer is bound to theantibody. However, in the presence of cAMP, the amount of bound tracerdecreases competitively with increasing concentrations of cAMP. The rateof molecular rotation of the tracer is much lower when the tracer isbound to antibody than when it is free in solution, so that thepolarization of light emitted by the tracer is higher when the tracer isbound to antibody than when it is free. Thus, the polarization decreasesas the amount of bound tracer decreases, allowing a quantification ofthe analyte cAMP, and hence any species that creates or degrades it.

1. Materials

Reagents may be provided separately or bundled together as a kit. Apreferred kit includes anti-cAMP antibody (100×), cAMP tracer(fluorescein-labeled cAMP, 100×), calibrator cAMP (500 mM), and assaybuffer.

Stock Final Concentration Reagent/Buffer Concentration in Assay PlatecAMP calibrator 1 mM 1:3 serial dilution in assay plate: (1 vial) 10,3.33, 1.11, 0.37. 0.12, 0.041, 0.014, & 0.005 μM cAMP antibody 300x1:300 dilution in assay plate (1 vial) cAMP tracer (1 vial) 500x 1:500dilution in assay plate Assay buffer (pH 7.6)The assay buffer should be stored refrigerated at 4° C., and theremaining reagents should be stored frozen at ≦−10° C. For optimalperformance, the antibody should not undergo repeated freeze/thawcycles, and the tracer should be protected from light. All reagentsshould be warmed to room temperature before use.

The tracer may be titrated before use to determine the optimal workingdilution for each application. The recommended dilution provides anintensity reading 5 to 6-fold higher than the assay buffer backgroundand allows the kit to be used for two 384-well microplates with 40 μLtotal assay volume per well or two 96-well microplates with 100 μL totalassay volume per well.

2. Equipment

The assay may be performed using any suitable sample holder, lightdetection device, and/or fluidics system, as described above. Apreferred sample holder (for supporting samples) is a microplate,particularly a COSTAR™ flat-bottom black microplate (Corning) or an LJLHE™ black microplate, among others. A preferred light detection device(for analyzing samples) is an ANALYST™ light-detection platform (LJLBioSystems, Inc.). A preferred fluidics system (for preparing samples)is an LJL ScreenStation™, as described in PCT Patent Application Ser.No. PCT/US00/12277, which is incorporated herein by reference.

3. Procedure

The following procedure uses 100 wells of a 384 well plate, withcalibrators and controls occupying up to 32 of the wells:

(1) Preparation of Reagents and Samples:

-   -   (a) Preparation of 1:75 cAMP antibody working stock. Dilute the        300× cAMP antibody stock 1:75 in cAMP assay buffer (0.05 M        HEPES, pH 7.5, 150 mM NaCl, 0.1% bovine gamma globulin) (e.g.,        by adding 14 μL of the 300× cAMP antibody stock to 1036 μL of        cAMP assay buffer). 10 μL of this working stock solution will be        added to the assay plate, as indicated in the plate layout in        FIG. 9.    -   (b) Preparation of cAMP tracer working stock. Dilute the 500×        cAMP tracer stock 1:125 in cAMP assay buffer (e.g., by adding 10        μL of the 500× cAMP tracer stock to 1240 μL of cAMP assay        buffer). 10 μL of this working stock solution will be added to        the assay plate, as indicated in the plate layout in FIG. 9.    -   (c) Preparation of cAMP calibration curve. Dilute the cAMP        calibrator 1:25 in cAMP assay buffer (e.g., by adding 10 μL cAMP        calibrator to 240 μL cAMP assay buffer) to give 10 μM cAMP        calibrator or 400 pmol in final assay. Prepare seven 1:3 serial        dilutions to give 3.33, 1.11, 0.37, 0.12, 0.041, 0.014, and        0.005 μM cAMP (133 to 0.125 pmol in final assay).    -   (d) Preparation of samples. Dilute samples as needed in cAMP        assay buffer. Prepare at least 25 μL of each dilution if        duplicates are to be run.        (2) Addition of Calibrators, Controls, and Samples to 384-Well        Plates.    -   Add calibrators, controls, and samples to the assay plate, as        indicated in the plate layout in FIG. 9. Preferably, titrations        should be performed in duplicate, and controls should be        performed in quadruplicate. Order of addition and incubation        time is very important.    -   (a) Add cAMP assay buffer to respective wells.    -   (b) Add cAMP working stock antibody to respective wells.    -   (c) Add cAMP calibrator or sample to respective wells.    -   (d) Add tracer to respective wells, mix gently, cover, and        incubate for 2 hours, shielded from room light. To further        increase assay performance, incubate the assay plate overnight        at 4° C., covered and shielded from light. A plastic plate cover        may be used to prevent possible evaporation, but care should be        taken with plastic plate sealers, which may introduce        undesirable background fluorescence.    -   (e) Read plate using a light detection device capable of        generating and detecting polarized light. A preferred light        detection device is an ANALYST™ light-detection platform, used        with the following parameter settings:

Parameter Setting Lamp Continuous Plate format Corning Costar 384 PSWells selected (Select data range) Z-height 2 mm G-factor 0.94(depending on instrument) Units Counts/sec Excitation 1 Fluorescein 485nm Emission 1 Fluorescein 530 nm Reading per well 1 Integration time200,000 Attenuator mode Out Dynamic polarizer Emission Static polarizerS Polarizer settling time 10 ms Shake time 0 sec Velocity 20 mm/secDiameter 5 mm Measurement type Comparator (sensitivity = 2-4) Platesettling time 50 ms

-   -   (f) Calculate background-corrected P values if desired, and plot        mP vs. pmol cAMP calibration curve, as described below.        4. Data Analysis

The data for the calibration curve can be analyzed using any suitablemethod, such as importing the data into an Excel spreadsheet foranalysis. To improve accuracy, polarizations should be computed usingcorrected sample intensities determined by subtracting backgroundintensities from the raw sample intensities, and not by computing rawsample polarizations and then subtracting background polarizations. Apreferred procedure is described below.

-   (1) Average both “S” and “P” intensity readings for the assay buffer    alone (wells 2A-D) and antibody alone (wells 2J-L). These are the    “buffer background” and “antibody background” values, respectively.-   (2) Subtract the “S” buffer background value from each individual    “S” value for the tracer (column 2, I-L, tracer only). Repeat to    correct the “P” intensity values of the tracer.-   (3) Subtract the “S” antibody background value from each individual    “S” value for the tracer bound to the antibody (column 2, E-H) and    from each of the values for the calibration curve and samples    (columns 1 and 3). Repeat to correct the “P” intensity values for    the above measurements.-   (4) Calculate the polarization (in milli-polarization “mP” units)    for the background-corrected data for columns 1, 2 (tracer only and    tracer+antibody), and 3 using the following formula:

$\begin{matrix}{P = {\frac{S - \left( {G \cdot P} \right)}{S + \left( {G \cdot P} \right)} \cdot {1000\mspace{11mu}\lbrack{mP}\rbrack}}} & (1)\end{matrix}$

-   -   Here, G is a “G factor,” which corrects for contributions of the        instrument light path to total polarization. In practice, G is        almost always close to unity, so it usually can be conveniently        set to this value without compromising the subsequent analysis.

-   (5) Average the individual values for columns 1, 2 (tracer only and    tracer+antibody), and 3.

-   (6) Plot the calibration curve. Calculate the IC50 concentration    (i.e., the concentration of the calibrator that gives a 50% decrease    in polarization from bound vs. free tracer), either from the data or    from the calibration curve.

Example 4

This example shows use of a calibration curve in a cAMP assay.Specifically, FIG. 10 shows a calibration curve for a cAMP assaymeasured using the reagents and methods of Example 4. The polarizationof the calibrator was computed after subtracting the appropriatebackground intensities, as described above. The cAMP concentration in anunknown sample is determined by matching the polarization measured forthe unknown with the cAMP concentration corresponding to thatpolarization in the calibration curve. The minimum detectableconcentration was about 0.1 pmol.

Example 5

This example shows use of a calibration curve in a cGMP assay.Specifically, FIG. 11 shows a calibration curve for a cGMP assayconducted using cGMP-based reagents and methods analogous to thosedescribed (for cAMP) in Example 4. The cGMP concentration in an unknownsample is determined by matching the polarization measured for theunknown with the cGMP concentration corresponding to that polarizationin the calibration curve. Here, the tracer isfluorescein-5-ITC-1,4-diaminocyclohexyl-2′-O-succinyl-GMP, and thespecific binding partner is an anti-cGMP antibody (Chemicon). Thecalibration curve shows that the change in polarization obtained usingthese reagents is smaller than the change in polarization obtained undersimilar conditions in FIG. 10 for cAMP; however, this change may beincreased by using different reagents, such as the tracer1,2-diaminocyclohexyl (DACH).

Example 6

This example shows another assay for adenylyl cyclase activity.Specifically, FIG. 12 shows activity of recombinant adenylyl cyclase inmembrane preparations, measured using (A) the reagents and methods ofExample 3, and (B) a standard radioactivity-based assay (FlashPlate™assay, New England Nuclear). The results show that the present assayperforms well in comparison with standard radioactivity-based assays.

Example 7

This example shows an assay for phosphodiesterase activity.Specifically, in a sample provided with a luminescent cAMP (or othercyclic nucleotide) tracer and a specific binding partner,phosphodiesterase will hydrolyze the cAMP to the correspondingmonophosphate, which should no longer bind to the specific bindingpartner. This will decrease the amount of tracer bound to the bindingpartner and concomitantly decrease the measured polarization.

Example 8

This example shows a method (and associated kit) for detecting cAMP andmodulators of receptors and enzymes that generate cAMP in whole cells.The following two protocols illustrate with the general adenylatecyclase activator forskolin an application of this assay, which may beapplied in combination with the assay of Example 3. The protocols havebeen developed for use with adherent or suspension cells. The procedurecould be modified for agonists or antagonists such as thebeta-adrenergic agonist isoproterenol or antagonist propranolol. FIG. 13illustrates both forskolin and agonists/antagonist detection for atypical assay. Forskolin causes the expected rise in cAMP in theadherent cell line T47D (following the protocol below for adherentcells). The beta-adrenergic agonist isoproterenol also stimulates cAMPproduction, via the endogenous beta receptors on the cells. Thisstimulation is reversed by addition of a beta adrenergic antagonist,propranolol.

(a) Adherent Cells

The following example is for adherent cells, for example, using theadherent cell line T-47D:

-   -   1) Culture cells (100 μL/well) in standard 96-well microtiter        plates (tissue culture grade) with cell concentration at        2.5-10×10⁵ cells/mL (25,000-100,000 cells/well).    -   2) Incubate plated cells overnight at 37° C. in a humidified        atmosphere of 5% CO₂: 95% air.    -   3) Gently aspirate off media, and slowly add 250 μL Krebs-Ringer        Bicarbonate Buffer with glucose, pH 7.4 (KRBG Buffer); use        multi-channel pipettor.    -   4) Gently aspirate off the KRBG and add 100 μL Stimulation        Buffer        -   Stimulation Buffer (containing 0.75 mM IBMX in KRBG Buffer;            make fresh on day of experiment).        -   10 mL KRBG Buffer (pH 7.4)        -   9.4 μL 800 mM IBMX    -   5) Incubate for 10 minutes at room temperature.    -   6) Add 50 μL 3× Forskolin or PBS. Gently mix and incubate at        37° C. for 15 minutes.        -   Forskolin, 3× (20 μM final concentration)        -   1500 μL PBS (pH 7.4) containing        -   3.0 μL 30 mM forskolin (60 μM stock)    -   7) Add lysis reagent, 4× LyX Buffer (50 μL). Agitate cells. This        is to facilitate cell lysis and can be achieved by shaking the        plate on a plate shaker for 10 minutes after adding the lysis        reagent.    -   4×Ly×Buffer    -   2% triton×−100    -   0.1% acetic acid    -   8) Lysed cells are now immediately processed in the HEFP cAMP        assay, using 10 μL neat, or suitably diluted in additional 1×        LyX lysis buffer.        (b) Suspended Cells

The following example is for cells in suspension, for example, using thecell line HEK 293. Cells are treated with 0.02% EDTA to gently detachcells. The entire assay (cell stimulation, lysis, and cAMP assay) wasperformed in a single 384-well plate:

-   -   1) Grow cells in T-75 or T-175 flasks to 85-90% confluency.    -   2) On the day of experiment, aspirate growth media, and rinse        cells with PBS.    -   3) Remove PBS, and add 1 to 2 mL 0.02% EDTA solution to detach        cells (Sigma, P/N 8008). To facilitate detachment of cells,        incubate for 3 to 5 minutes at 37° C.    -   4) Resuspend cells by adding 10 mL growth media to cell        suspension. Count cells, and then centrifuge the cells at        1000-1500×g for 5 minutes to form a pellet.    -   5) Wash cell pellet once with KRBG.    -   6) Resuspend cells in Stimulation Buffer to desired density        (e.g., 1×10⁶ cells/mL will give 5,000 cells/well if 5 μL/well        are dispensed in a 384-well plate). Incubate for 10 minutes at        room temperature.        -   Stimulation Buffer (containing 0.75 mM IBMX in KRBG Buffer;            make fresh on day of experiment).        -   10 mL KRBG Buffer (pH 7.4)        -   9.4 μL 800 mM IBMX    -   7) Dispense 5 μL cell suspension to wells in a 384-well plate.    -   8) Add 10 μL 1.5× forskolin or PBS to the cells in suspension.        Gently mix, and incubate at 37° C. for 15 minutes.        -   Forskolin. 1.5× (20 μM final concentration)        -   3000 μL PBS (pH 7.4) containing        -   3.0 μL of 30 mM forskolin (30 μM stock)    -   9) Add 5 μL 4× LyX Buffer to the cells, and incubate for 10        minutes to terminate the stimulation and to lyse the cells. To        facilitate cell lysis, place plate on a plate shaker for 10        minutes after adding the lysis reagent.    -   10) Add 10 μL Antibody followed by 10 μL Tracer for HEFP        detection directly in the wells, and incubate as desired (e.g.,        as indicated in Example 3). Be sure to include any necessary        controls and/or calibration curve.

Example 9

This example shows an assay for cAMP and selected modulators ofreceptors and enzymes that generate cAMP in whole cells. Specifically,FIG. 13 shows the effects of various modulators on cAMP levels incultured T47D cells, measured using the reagents and methods of Examples3 and 8. Here, T47D cells were washed and treated according to theprotocol in Example 8. The cells were incubated for a predeterminedperiod, and then lysed. Polarization reagents were added, and the samplewas examined using an ANALYST™ light-detection platform (LJL BioSystems,Inc.) according to relevant portions of the protocol in Example 3. Theresults show that the assay responds as expected to agents that modulatecAMP production. In particular, cAMP production was stimulated byforskolin and isoproterenol, and inhibited by propranolol. Forskolin isa known nonspecific stimulator of adenylyl cyclase. Isoproterenol is abeta-adrenergic agonist that stimulates cAMP production by thereceptor's normal specific coupling to adenylyl cyclase.

Example 10

This example shows assays for hormones whose cellular responses aremediated by cAMP. Specifically, the assays described here for cAMP maybe used to measure the presence and/or activity of the followinghormones, among others.

Selected Hormone-induced Cellular Responses Mediated by cAMP TargetTissue Hormone Major Response Thyroid gland Thyroid-stimulating hormoneThyroid hormone (TSH) synthesis and secretion Adrenal cortexAdrenocorticotropic hormone Cortisol secretion (ACTH) Ovary Luteinizinghormone (LH) Progesterone secretion Muscle Adrenaline Glycogen breakdownBone Parathormone Bone resorption Heart Adrenaline Increase in heartrate and force of contraction Liver Glucagon Glycogen breakdown KidneyVasopressin Water resorption Fat Adrenaline, ACTH, Triglyceridebreakdown glucagon, TSH

Example 11

This example shows a direct assay for cell-signaling receptors.Specifically, a labeled ligand may be selected that binds specificallyto an activated form of a receptor. The labeled ligand, then, willexhibit a shift in luminescence polarization when bound to the activatedreceptor. The assay also can be constructed to assess the concentrationof activated receptor in a sample. This can be done in the context ofmembrane or tissue samples or in a cellular suspension. An increase inthe polarization of emitted luminescence will be correlated with theconcentration of activated receptor in the sample.

An example of such a labeled ligand is a nonhydrolyzable (stabilized)analog of GTP, such as FI-GTP(γ-S), where FI denotes a luminophore. GTPand other specific guanine nucleotide forms bind to the activated formsof a class of receptors variously known as G-protein-coupled receptors,serpentine receptors, seven-pass transmembrane receptors, and 7transmembrane-spanning domain receptors. The GTP(γ-S) (or othernonhydrolyzable form) is labeled with the luminophore (such asfluorescein) such that the GTP(γ-S) still retainsactivated-receptor-binding properties. Activation of the relevantreceptor, such as the thrombin receptor or the various opioid receptors,can then be measured in an appropriately designed assay, for example, bymeasuring the increase in polarization associated with binding. Anonhydrolyzable GTP analog will tend to remain bound to the receptorlonger than GTP itself, facilitating measurement of the binding.

As described above, the nonpeptide tracer moiety also may be a productof the activation of a receptor, such as cAMP or cGMP. Labeled forms ofthese secondary messengers are useful in assays to determine signalinglevels by establishing competing binding for an antibody or otherspecific binding pair member between the labeled tracer and the cAMP orcGMP generated from the receptor activation.

These assays also can be used to determine the ability of candidatedrugs to affect the level of activation of a receptor. The luminescencepolarization assay is performed in the presence and the absence of thecandidate drug. Drugs that interfere with the activation of the receptorwill diminish the level of enhanced polarization.

Example 12

This example shows a general assay for activation of GTP-bindingproteins. Specifically, the labeled ligand of Example 11 may be used toassay for the activation of any GTP-binding protein, based on thedecrease in polarization that will accompany binding of the luminescentanalog of GTP to the GTP-binding proteins during activation. SuitableGTP-binding proteins include the trimeric G-proteins and the Rassuperfamily of monomeric GTPases, among others.

Example 13

This example shows assays for trimeric G-proteins. Specifically, theassays of Examples 11 and 12 may be used to measure the presence and/oractivity of the following G-proteins, among others.

Major Families of Trimeric G-Proteins Effects of Selected Selected αBacterial Family Examples Subunits Functions Toxins I G_(s) α_(s)Activates Cholera adenylyl cyclase activates Activates Ca²⁺ channelsG_(olf) α_(olf) Activates adenylyl Cholera cyclase in olfactoryactivates sensory neurons II Gi α_(i) Inhibits adenylyl cyclasePertussis Activates K⁺ channels inhibits G_(o) α_(o) Activates K⁺channels Pertussis Inactivates Ca²⁺ inhibits channels Activatesphospholipase C-β G_(t) α_(t) Activates cGMP Cholera (transducin)phosphodiesterase in activates vertebrate rod Pertussis photoreceptorsinhibits III G_(q) α_(q) Activates phospholipase No effect C-β

Example 14

This example shows assays for components of the inositol-phospholipidsignaling pathway, including associated G-proteins. Generally, theassays include luminescence polarization assays directed tointermediates of this pathway, such as 1,4,5 IP3. The assays include atracer form of the intermediate and a specific binding partner of theintermediate and tracer. The tracer may include a luminophore attachedby a suitable chemistry to the intermediate (such as a fluoresceinsuccinyl-labeled IP3). The binding partner may include an antibody thatspecifically binds to the intermediate and tracer. Assays may beperformed as shown in FIG. 5, with the intermediate taking the place ofthe cyclic nucleotide. Assays for associated G-proteins may be performedas shown in FIG. 6. These assays may be used to measure the presence,concentration, and/or activity of intermediates, enzymes, and/orreceptors involved in this pathway, or they may be directed toassociated tissues and responses, as indicated in the following table:

Selected Hormone-induced Cellular Responses Mediated by G-Protein-linkedReceptors Coupled to the Inositol- Phospholipid Signal Pathway TargetTissue Signaling Molecule Major Response Liver Vasopressin Glycogenbreakdown Pancreas Acetylcholine Amylase secretion Smooth muscleAcetylcholine Contraction Mast cells Antigen Histamine secretion Bloodplatelets Thrombin Aggregation

Example 15

This example shows assays for integrated cell signaling mechanisms.Specifically, the assays described here for cyclic nucleotides andGTP-binding proteins may be performed together and/or performed incombination with the kinase assays described in the PCT PatentApplication Ser. No. PCT/US00/16025, filed Jun. 9, 2000, which isincorporated herein by reference. Such combination assays permit studyof signaling mechanisms involving multiple pathways.

Example 16

This example shows assays with improved signals, signal-to-noise ratios,and/or signal-to-background ratios.

Signal may be enhanced in several ways, including (1) using a high colortemperature light source, such as a xenon arc lamp, in a continuousillumination mode, (2) using a dichroic or multi-dichroic beamsplitter,and/or (3) using a sample holder whose shape is “matched” to the shapeof the optical beam of the instrument, especially if the sample holderis elevated to bring the sample closer to a detector. The high colortemperature light source increases the number of usable photons, whichis important because the lower limit of the signal-to-noise ratio is setby the square root of the total number of photons collected in themeasurement. These enhancements are described in more detail in thefollowing U.S. patent applications, which are incorporated herein byreference: Ser. No. 09/349,733, Ser. No. 09/478,819, and Ser. No.09/494,407.

Signal-to-noise ratios can be enhanced at least in part by increasingsignals, for example, by using the techniques described in the previousparagraph.

Signal-to-background ratios can be enhanced in several ways, including(1) using confocal optical systems having a sensed volume to avoidluminescence from the microplate walls, (2) selecting a microplate orother substrate that increases the signal and reduces the luminescentbackground from materials in the microplate, (3) selecting the lightsources, luminescence filters, optics, signal collection electronics,and mechanical system used in the luminescence detection optical systemfor maximum signal-to-background ratio, and (4) utilizing signalprocessing, background subtraction, and luminescence lifetimetechniques, particularly FLAMe™ methodology for background reduction, asdescribed below. These enhancements are described in more detail in thefollowing U.S. patent and U.S. patent applications, which areincorporated herein by reference: U.S. Pat. No. 6,071,748, Ser. No.09/349,733, Ser. No. 09/478,819, and Ser. No. 09/494,407.

Example 17

This example shows mechanisms for increasing the change in polarizationthat accompanies a change in binding, so that the change in binding canbe measured more easily. These mechanisms may be used in any of theassays described here involving luminescently labeled species, such aslabeled cyclic nucleotides and labeled nonhydrolyzable GTP analogs,among others.

The change in polarization upon binding can be increased by making anylinker between the luminophore and the labeled species (e.g., the cyclicnucleotide or GTP analog) as short and/or rigid as possible, whilemaintaining relevant substrate properties for the enzymes involved inthe assay. Short and/or rigid linkers will restrict luminophore motionrelative to the labeled species, reducing the “propeller effect” so thatthe luminophore more accurately reports the motion of both the free andbound labeled species. The rigidity of the linker may be increased byavoiding using hexanoic acid linkers, which typically are long andflexible, and by using cyclic linkers and amide groups in place ofmethylene groups, among other mechanisms.

The change in polarization upon binding also can be increased byincluding an appropriately positioned energy transfer acceptor on thebinding partner, so that energy transfer will occur from the luminophoreto the acceptor upon incorporation. Such energy transfer will shortenthe lifetime of the luminophore, thereby increasing its polarization(because polarization varies inversely with lifetime, all else beingequal).

The change in polarization upon binding also can be increased bydecreasing the mobility of the binding partner for the labeled species.Mobility can be decreased by increasing the size of the binding partner,either directly or by forming a complex with a mass label. Suitable masslabels include other molecules and beads, among others. The use of masslabels is described in detail in PCT Patent Application Ser. No.PCT/US99/24707, which is incorporated herein by reference. Mobility alsocan be decreased by attaching the binding partner to a surface, such asthe surface of a sample holder. Attachment to other molecules, beads,and/or surfaces may be accomplished using any of a number of well-knownreactive groups.

Example 18

This example describes principles of luminescence polarization assays.Here, luminescence refers to the absorption and subsequent re-emissionof light by a luminescent molecule, or “luminophore,” and polarizationrefers to the direction of the light's electric field, which generallyis perpendicular to the direction of the light's propagation. In aluminescence polarization assay, specific molecules within a compositionare labeled with one or more luminophores. The composition then isilluminated with polarized excitation light, which preferentiallyexcites luminophores having absorption dipoles aligned parallel to thepolarization of the excitation light. These molecules subsequently decayby preferentially emitting light polarized parallel to their emissiondipoles. The extent of polarization of the total emitted light dependson the extent of molecular reorientation during the time intervalbetween luminescence excitation and emission, which is termed theluminescence lifetime, τ. In turn, the extent of molecular reorientationdepends on the luminescence lifetime and the size, shape, andenvironment of the reorienting molecule. Thus, luminescence polarizationassays may be used to quantify binding reactions and enzymatic activity,among other applications. In particular, molecules commonly rotate (or“tumble”) via diffusion, with a rotational correlation time τ_(rot) thatis proportional to their volume, or the cube of their radius ofgyration. (This cubic dependence on radius makes polarization assaysvery sensitive to binding.) Thus, during their luminescence lifetime,relatively large molecules will not reorient significantly, so thattheir total luminescence will be relatively polarized. In contrast,during the same time interval, relatively small molecules will reorientsignificantly, so that their total luminescence will be relativelyunpolarized.

The relationship between polarization and intensity is expressed by thefollowing equation:

$\begin{matrix}{P = \frac{I_{\parallel} - I_{\bot}}{I_{\parallel} + I_{\bot}}} & (2)\end{matrix}$Here, P is the polarization, I_(∥) is the intensity of luminescencepolarized parallel to the polarization of the excitation light, andI_(⊥) is the intensity of luminescence polarized perpendicular to thepolarization of the excitation light. P generally varies from zero toone-half for randomly oriented molecules (and zero and one for alignedmolecules). If there is little rotation between excitation and emission,I_(∥) will be relatively large, I_(⊥) will be relatively small, and Pwill be close to one-half. (P may be less than one-half even if there isno rotation; for example, P will be less than one-half if the absorptionand emission dipoles are not parallel.) In contrast, if there issignificant rotation between absorption and emission, I_(∥) will becomparable to I_(⊥), and P will be close to zero. Polarization often isreported in milli-P units (1000×P), which for randomly orientedmolecules will range between 0 and 500, because P will range betweenzero and one-half.

Polarization also may be described using other equivalent quantities,such as anisotropy. The relationship between anisotropy and intensity isexpressed by the following equation:

$\begin{matrix}{r = \frac{I_{\parallel} - I_{\bot}}{I_{\parallel} + {2I_{\bot}}}} & (3)\end{matrix}$Here, r is the anisotropy. Polarization and anisotropy include the sameinformation, although anisotropy may be more simply expressed forsystems containing more than one luminophore. In the description andclaims that follow, these terms may be used interchangeably, and ageneric reference to one should be understood to imply a genericreference to the other.

The relationship between polarization and rotation is expressed by thePerrin equation:

$\begin{matrix}{\left( {\frac{1}{P} - \frac{1}{3}} \right) = {\left( {\frac{1}{P_{0}} - \frac{1}{3}} \right) \cdot \left( {1 + \frac{\tau}{\tau_{rot}}} \right)}} & (4)\end{matrix}$Here, P₀ is the polarization in the absence of molecular motion(intrinsic polarization), τ is the luminescence lifetime (inverse decayrate) as described above, and τ_(rot) is the rotational correlation time(inverse rotational rate) as described above.

The Perrin equation shows that luminescence polarization assays are mostsensitive when the luminescence lifetime and the rotational correlationtime are similar. Rotational correlation time is proportional tomolecular weight, increasing by about 1 nanosecond for each 2,400 daltonincrease in molecular weight (for a spherical molecule). For shorterlifetime luminophores, such as fluorescein, which has a luminescencelifetime of roughly 4 nanoseconds, luminescence polarization assays aremost sensitive for molecular weights less than about 40,000 daltons. Forlonger lifetime probes, such as Ru(bpy)₂dcbpy (ruthenium2,2′-dibipyridyl 4,4′-dicarboxyl-2,2′-bipyridine), which has a lifetimeof roughly 400 nanoseconds, luminescence polarization assays are mostsensitive for molecular weights between about 70,000 daltons and4,000,000 daltons.

Luminescence polarization assays may be used in a variety of formats. Inone format, the concentration of an analyte in solution can be measuredby supplying a labeled tracer that competes with the analyte for abinding moiety, particularly a binding moiety larger than the labeledtracer. In this “competitive” format, the concentration of the analyteis inversely correlated with the enhancement of luminescencepolarization in the light emitted by the tracer when it competitivelybinds the common moiety. In another format, the concentration of atarget can be measured by supplying a labeled tracer that is capable ofbinding the target. In this case, the enhancement of polarization is adirect measure of the concentration of target. The target further maybe, for example, an activated receptor, where activation can beindirectly measured by the directly measured concentration of agenerated molecule or by its binding to labeled tracer per se.

Although the invention has been disclosed in its preferred forms, thespecific embodiments thereof as disclosed and illustrated herein are notto be considered in a limiting sense, because numerous variations arepossible. As used herein, singular terms do not preclude the use of morethan one of the associated element, and embodiments using more than oneof a particular element are within the spirit and scope of theinvention. Applicants regard the subject matter of their invention toinclude all novel and nonobvious combinations and subcombinations of thevarious elements, features, functions, and/or properties disclosedherein. No single feature, function, element or property of thedisclosed embodiments is essential. The following claims define certaincombinations and subcombinations of features, functions, elements,and/or properties that are regarded as novel and nonobvious. Othercombinations and subcombinations may be claimed through amendment of thepresent claims or presentation of new claims in this or a relatedapplication. Such claims, whether they are broader, narrower, equal, ordifferent in scope to the original claims, also are regarded as includedwithin the subject matter of applicants' invention.

We claim:
 1. A method of testing a compound for modulation of a receptoror enzyme involved in generation of a cyclic nucleotide, the methodcomprising: contacting a sample with a tracer comprising a cyclicnucleotide coupled to a luminophore, and with an opposite member of aspecific binding pair to the cyclic nucleotide; illuminating the samplewith polarized light, wherein the light is capable of inducing emissionof polarized light from the luminophore; measuring the extent ofpolarization of light emitted from the luminophore in the presence andin the absence of a compound; and identifying the compound as amodulator of the receptor or enzyme if the extent of polarizationchanges in the presence relative to the absence of the compound.
 2. Themethod of claim 1, wherein the step of identifying includes a step ofidentifying the compound as an inhibitor of the receptor or enzyme ifthe extent of polarization increases in the presence relative to theabsence of the compound.
 3. The method of claim 1, wherein the step ofidentifying includes a step of identifying the compound as an activatorof the receptor or enzyme if the extent of polarization decreases in thepresence relative to the absence of the compound.
 4. The method of claim1, wherein the step of measuring the extent of polarization of lightcomprises a step of evaluating a function selected from the groupconsisting of polarization and anisotropy.
 5. The method of claim 1,wherein the opposite member of a specific binding pair is an antibody.6. The method of claim 1, wherein the nucleotide is cyclic AMP (cAMP) orcyclic GMP (cGMP).
 7. The method of claim 6, wherein the nucleotide iscyclic AMP (cAMP).
 8. The method of claim 6, wherein the nucleotide iscyclic GMP (cGMP).
 9. The method of claim 1, wherein the step ofcontacting includes a step of contacting whole cells or a cell lysatewith the compound.
 10. The method of claim 1, wherein the step ofidentifying includes a step of identifying the compound as an inhibitoror activator of a G-protein-coupled receptor.
 11. The method of claim 1,wherein the step of identifying includes a step of identifying thecompound as an inhibitor or activator of adenylyl cyclase.
 12. Themethod of claim 1, wherein the step of identifying includes a step ofidentifying the compound as an inhibitor or activator of guanylylcyclase.
 13. The method of claim 1, further comprising a step ofproviding the tracer in a lysis buffer.